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Tags

A tag is a keyword or label that categorizes your question with other, similar questions. Using the right tags makes it easier for others to find and answer your question.

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Please supplement your question with a minimal reproducible example. Use dput() for data and specify all non-base packages with library calls. For statistical questions please use http://stats.stackex…
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if they pertain to issues related to bioinformatics analysis of RNA-seq data, e.g. normalization, differential expression analysis, sequencing and experimental design…
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a programming language, widely used in bioinformatics
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about sequence alignment.
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one of the common binary formats used to store sequence alignment information. Questions should include this tag if they directly pertain to the format itsel…
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for questions related to single-cell RNA-seq.
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Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.
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to refer to the gene sequence/coding part of the sequence.
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should be used for questions specific to sequence file format `.fasta`. should **not** be used if you just used fasta file, or if the question is more general about sequence formats.
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organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.
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The process of connecting a sequence of nucleotide to its function or special features. For example, annotating a genome consists in finding where the genes are, the promoters, enhancers, special repe…
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a text file type used to store information regarding genetic variants.
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Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.
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to refer to the alignment of dna/protein sequences alignment i.e arranging sequences in order to find similarity between sequences.
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the process of determining the precise order of nucleotides within a DNA molecule.
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use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific …
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for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.
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a set of freely available tools for biological computation written in Python.
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Single Nucleotide Polymorphisms. How to find them? How to correlate them with other data? How to represent them? What is their distribution?
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for questions about how to use, download, retrieve, check and browse public databases.
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Questions asking whether a software exists for a certain purpose; questions asking which software is best among a selection for a certain purpose.
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Questions specific to interacting with and post-processing sequence alignments using the SAMtools package. For questions specifically about formats SAM, BAM or CRAM use tags sam or bam,
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For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
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Questions specific to nanopore sequencing. For general question about long reads, use tag long-reads instead and for questions about specific sequencer use a specific sequencer tag (i.e. minion, gridi…
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sets of defined rules to organise a specific type of data. Common file format in bioinformatics include FASTA, FASTQ, SAM, BAM, VCF.
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Basic Local Alignment Search Tool: algorithm that finds regions of similarity between a pair of sequences, can be used to query an unknown sequence against a database of known sequences.
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Process of creating the original sequence from the read sequences that it generated during a sequencing experiment. Can refer to genome assembly, in which case the original sequence is a genome, or tr…
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When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).
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Use it when comparing a measure of the expression between two (or more) samples, where the units are relative to the comparison.
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a file format use to store short reads and their quality values
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The process of discovering variants in individuals starting from sequencing reads. Can be subdivided into germline variant calling and somatic variant calling. Can also be used for the more specific p…
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A file format used in structural biology to describe the 3-D coordinates of atoms of a biological structure, often a protein. Can also refer to the Protein Data Bank database, which stores all the sub…
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The set of all transcripts of a biological entity, e.g. the transcriptome of a single cell, of a tissue, of an organ, of an individual, of a species. Can also be used to refer to a subset of the trans…
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Browser Extensible Data, a collection of related plain text formats for describing genome features for visualization with genome browsers.